Populations of genital tract viruses distinct from the blood have been reported in men and women. Variations of immune and drug pressures across physical barriers and variations in cellular physiology may result in unequal levels of viral replication and selective forces between anatomically distinct sites. However, whether distinct HIV-1 genotypes and phenotypes distinguish viruses in the genital tract compared to the blood of women has not been completely defined. Understanding whether viruses evolve independently within the genital tract, the usual anatomic site involved in HIV-1 transmission, is critical for optimizing treatment and designing vaccines. We have observed that HIV-1 infected cells may proliferate, more so in the genital tract compared to the blood. In the genital tract of women, proliferation of cells with proviruses is probably due to exposures to infections and to traumas (e.g., sexual intercourse, tampons, etc.). This proliferation may be an obstacle to curing HIV-1 infection. The studies we propose aim to describe the generation of viruses in the genital tract and the interplay of blood and genital tract viruses in ART-treated and untreated women. The overarching hypotheses of this proposal are that: (1) The female genital tract is not a virologic compartment distinct from the blood. Rather, HIV-1 in the genital mucosa is in large part temporally related to viruses in the blood, with which it traffics freely. (2) HIV-1 viral diversity is greater in the genital tract compared to the blood, and thus the genital tract behaves as a viral reservoir from which new viral genotypes originate. (3) Clonally expanded populations of HIV-1 infected cells often comprise the majority of genital tract HIV-1 DNA. Our specific aims test these hypotheses: 1: Determine whether female genital tract viruses form lineages that are discrete from the blood. 2: Determine if the female genital tract is a viral reservoir and a frequent source of viruses rebounding in the plasma when ART is stopped or during virologic failure of ART with the selection of drug-resistant virus. 3: Determine if monotypic (identical) HIV-1 env sequences in the blood and uterine cervix result from proliferation of infected cells or from bursts of viral replication. PUBLIC HEALTH RELEVANCE: Over half of all HIV-1 infected people worldwide are women. HIV-1 is present in the genital tract, where it may pose a risk of transmission to sexual partners. We have observed that HIV-1 populations may grow in the genital tract because cells with virus proliferate in the genital tract, probably due to exposures to infection and trauma (e.g., sexual intercourse, tampons, etc.) This proliferation may be an obstacle to curing HIV-1 infection.